We integrate the public datasets Tyser (1195 cells, Human) and Zhai CS8 (11629 cells, Macaca) following both the standard CCA integration approach and the RPCA approach.
Visualization of the different clustering resolutions of the integrated reference
Visualization of the different clustering resolutions of the integrated reference
## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Rocky Linux 8.7 (Green Obsidian)
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## Matrix products: default
## BLAS/LAPACK: /flask/apps/eb/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0
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## locale:
## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] viridis_0.6.4 viridisLite_0.4.2 clustree_0.5.0 ggraph_2.1.0
## [5] cowplot_1.1.1 scales_1.2.1 ggpubr_0.6.0 patchwork_1.1.2
## [9] SeuratObject_4.1.3 Seurat_4.3.0.1 glue_1.6.2 DT_0.28
## [13] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
## [17] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
## [21] ggplot2_3.4.2 tidyverse_2.0.0 here_1.0.1
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## loaded via a namespace (and not attached):
## [1] readxl_1.4.3 backports_1.4.1 plyr_1.8.8
## [4] igraph_1.5.0.1 lazyeval_0.2.2 sp_2.0-0
## [7] splines_4.2.0 listenv_0.9.0 scattermore_1.2
## [10] digest_0.6.33 htmltools_0.5.5 fansi_1.0.4
## [13] checkmate_2.2.0 magrittr_2.0.3 tensor_1.5
## [16] cluster_2.1.4 ROCR_1.0-11 tzdb_0.4.0
## [19] globals_0.16.2 graphlayouts_1.0.0 matrixStats_1.0.0
## [22] timechange_0.2.0 spatstat.sparse_3.0-2 colorspace_2.1-0
## [25] ggrepel_0.9.3 xfun_0.39 jsonlite_1.8.7
## [28] progressr_0.13.0 spatstat.data_3.0-1 survival_3.5-5
## [31] zoo_1.8-12 polyclip_1.10-4 gtable_0.3.3
## [34] leiden_0.4.3 car_3.1-2 future.apply_1.11.0
## [37] abind_1.4-5 rstatix_0.7.2 spatstat.random_3.1-5
## [40] miniUI_0.1.1.1 Rcpp_1.0.11 xtable_1.8-4
## [43] reticulate_1.30 htmlwidgets_1.6.2 httr_1.4.6
## [46] RColorBrewer_1.1-3 ellipsis_0.3.2 ica_1.0-3
## [49] pkgconfig_2.0.3 farver_2.1.1 sass_0.4.7
## [52] uwot_0.1.16 deldir_1.0-9 utf8_1.2.3
## [55] labeling_0.4.2 tidyselect_1.2.0 rlang_1.1.1
## [58] reshape2_1.4.4 later_1.3.1 cellranger_1.1.0
## [61] munsell_0.5.0 tools_4.2.0 cachem_1.0.8
## [64] cli_3.6.1 generics_0.1.3 broom_1.0.5
## [67] ggridges_0.5.4 evaluate_0.21 fastmap_1.1.1
## [70] yaml_2.3.7 goftest_1.2-3 knitr_1.43
## [73] fitdistrplus_1.1-11 tidygraph_1.2.3 RANN_2.6.1
## [76] pbapply_1.7-2 future_1.33.0 nlme_3.1-162
## [79] mime_0.12 compiler_4.2.0 rstudioapi_0.15.0
## [82] plotly_4.10.1 png_0.1-8 ggsignif_0.6.4
## [85] spatstat.utils_3.0-3 tweenr_2.0.2 bslib_0.5.0
## [88] stringi_1.7.12 highr_0.10 lattice_0.21-8
## [91] Matrix_1.6-0 vctrs_0.6.3 pillar_1.9.0
## [94] lifecycle_1.0.3 spatstat.geom_3.2-4 lmtest_0.9-40
## [97] jquerylib_0.1.4 RcppAnnoy_0.0.21 data.table_1.14.8
## [100] irlba_2.3.5.1 httpuv_1.6.11 R6_2.5.1
## [103] promises_1.2.0.1 KernSmooth_2.23-22 gridExtra_2.3
## [106] parallelly_1.36.0 codetools_0.2-19 MASS_7.3-60
## [109] rprojroot_2.0.3 withr_2.5.0 sctransform_0.3.5
## [112] parallel_4.2.0 hms_1.1.3 grid_4.2.0
## [115] rmarkdown_2.23 carData_3.0-5 Rtsne_0.16
## [118] spatstat.explore_3.2-1 ggforce_0.4.1 shiny_1.7.4